A cultivated rice species, Oryza sativa, has been widely believed that it speciated from Oryza rufipogon, the most closely related wild relative. With the phenotypic similarities to extant O. rufipogon accessions, two typical cultivated subspecies of O. sativa (indica and japonica) have been considered that each of them has speciated independently and is a corresponding descendent of each speciation event. However, exact status of divergence and evolutionary process of O. rufipogon is not yet explored in detail. To have a concept about evolutionary origins and process of cultivated rice, three typical accessions of O. rufipogon (W0106, W1921 and W1943) and two subspecies of cultivated O. sativa (indica and japonica) have been employed. From the viewpoint of phenotypic similarities, W0106 and W1921 show annual ecotype with indica-like phenotypes, while W1943 shows perennial ecotype with japonica-like phenotypes. Their genome short reads by Illumina GAIIx were preprocessed by a custom QV-filtering program and mapped on reference genome by BWA. Read depths and coverage length of each genome were calculated and SNPs and INDELs of commonly mapped regions in all accessions were counted. Those genotypes were used for haplotype analysis and comparison of genome structures among all five accessions. The results showed indica and japonica subspecies of O. sativa were descended from at least two lineages of O. rufipogon, and their phenotypic differences coincide with their genotypic profiles. Detail structural variations and phylogenetic relationships among them will be discussed in relation to species diversification, and evolutionary history.